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Background: Malaysia has already achieved remarkable accomplishments in reaching zero indigenous human malaria cases in 2018. Prompt malaria diagnosis, surveillance and treatment played a key role in the country's elimination success. Looking at the dynamics of malaria distribution during the last decades might provide important information regarding the potential challenges of such an elimination strategy. This study was performed to gather all data available in term of prevalence or incidence on Plasmodium infections in Malaysia over the last four decades. Methods: A systematic review of the published English literature was conducted to identify malaria distribution from 1980 to June 2019 in Malaysia. Two investigators independently extracted data from PubMed, Scopus, Web of Science and Elsevier databases for original papers. Results: The review identified 46 epidemiological studies in Malaysia over the 39-year study period, on which sufficient information was available. The majority of studies were conducted in Malaysia Borneo (31/46; 67.4%), followed by Peninsular Malaysia (13/46; 28.3%) and in both areas (2/46; 4.3%). More than half of all studies (28/46; 60.9%) were assessed by both microscopy and PCR. Furthermore, there was a clear trend of decreases of all human malaria species with increasing Plasmodium knowlesi incidence rate throughout the year of sampling period. The summary estimates of sensitivity were higher for P. knowlesi than other Plasmodium species for both microscopy and PCR. Nevertheless, the specificities of summary estimates were similar for microscopy (40–43%), but varied for PCR (2–34%). Conclusions: This study outlined the epidemiological changes in Plasmodium species distribution in Malaysia. Malaria cases shifted from predominantly caused by human malaria parasites to simian malaria parasites, which accounted for the majority of indigenous cases particularly in Malaysia Borneo. Therefore, malaria case notification and prompt malaria diagnosis in regions where health services are limited in Malaysia should be strengthened and reinforced to achieving the final goal of malaria elimination in the country. [ABSTRACT FROM AUTHOR]